Table 2.
Gene cluster analysis of transcriptome difference of BSGX001 (thi2Δ) vs. BSGX001 at the GX stage in the aspect of Molecular Function and Biological Processes.
| GOID | GO terms (Molecular Function) | Frequency | Gene(s) |
|---|---|---|---|
| UP-REGULATED | |||
| 3674 | Molecular function unknown | 34 out of 93 genes, 36.6% | ATS1, MAK16, BOL1, BOL3, AIM2, ECM1, ERP1, PAU7, YAR023C, UIP3, MST28, YAR064W, YAR066W, YAR068W, RRT6, SPG1, RGI2, FAR10, ARV1, SYM1, YLR255C, TMA7, YLR264C-A, BOP2, CMG1, SMD2, YLR281C, YLR283W, YLR287C, COQ11, SPH1, NKP2, PEX30, YLR326W |
| 16787 | Hydrolase activity | 14 out of 93 genes, 15.1% | CCR4, POP5, PHO11, YIL082W-A, CDC42, GPN3, CDD1, IRC20, MCM5, DBP9, CTS1, TAD3, SFH1, YRF1-6 |
| 3677 | DNA binding | 11 out of 93 genes, 11.8% | TFC3, SAW1, ECM22, EST1, RED1, NEJ1, PDR8, MCM5, YLR278C, MEC3, EST2 |
| 16740 | Transferase activity | 9 out of 93 genes, 9.7% | SWD1, YAT1, YIL082W-A, ERF2, IRC20, STT4, UBC12, EST2, GAS2 |
| 30234 | Enzyme regulator activity | 8 out of 93 genes, 8.6% | GIP4, CLN3, PEX22, GPB2, BUD14, RFU1, PIG1, GCD7 |
| 5198 | Structural molecule activity | 7 out of 93 genes, 7.5% | NUP60, RED1, RPS28B, MRPL15, RPL38, RPS25B, RPP0 |
| 3723 | RNA binding | 7 out of 93 genes, 7.5% | POP5, YIL082W-A, EST1, DBP9, GCD7, YHC1, RPP0 |
| 3735 | Structural constituent of ribosome | 5 out of 93 genes, 5.4% | RPS28B, MRPL15, RPL38, RPS25B, RPP0 |
| 4386 | Helicase activity | 4 out of 93 genes, 4.3% | IRC20, MCM5, DBP9, YRF1-6 |
| 16887 | ATPase activity | 3 out of 93 genes, 3.2% | MCM5, DBP9, SFH1 |
| 4518 | Nuclease activity | 3 out of 93 genes, 3.2% | CCR4, POP5, YIL082W-A |
| 1071 | Nucleic acid binding transcription factor activity | 3 out of 93 genes, 3.2% | TFC3, ECM22, PDR8 |
| 3682 | Chromatin binding | 3 out of 93 genes, 3.2% | RED1, YCS4, MCM5 |
| 5085 | Guanyl-nucleotide exchange factor activity | 3 out of 93 genes, 3.2% | EFB1, LTE1, GCD7 |
| 19899 | Enzyme binding | 2 out of 93 genes, 2.2% | VPS8, GIP4 |
| 3729 | mRNA binding | 2 out of 93 genes, 2.2% | DBP9, YHC1 |
| 16779 | nucleotidyltransferase activity | 2 out of 93 genes, 2.2% | YIL082W-A, EST2 |
| 4871 | Signal transducer activity | 2 out of 93 genes, 2.2% | GPB2, MID2 |
| 43167 | Ion binding | 2 out of 93 genes, 2.2% | RBG1, NUP60 |
| 3924 | GTPase activity | 2 out of 93 genes, 2.2% | CDC42, GPN3 |
| 22857 | Transmembrane transporter activity | 2 out of 93 genes, 2.2% | THI7, CSC1 |
| 8135 | Translation factor activity, RNA binding | 1 out of 93 genes, 1.1% | GCD7 |
| 16491 | Oxidoreductase activity | 1 out of 93 genes, 1.1% | BDH2 |
| 16798 | Hydrolase activity, acting on glycosyl bonds | 1 out of 93 genes, 1.1% | CTS1 |
| 8233 | Peptidase activity | 1 out of 93 genes, 1.1% | YIL082W-A |
| 16853 | Isomerase activity | 1 out of 93 genes, 1.1% | ECI1 |
| 16301 | Kinase activity | 1 out of 93 genes, 1.1% | STT4 |
| 988 | Transcription factor activity, protein binding | 1 out of 93 genes, 1.1% | TFC3 |
| 30674 | Protein binding, bridging | 1 out of 93 genes, 1.1% | ATG39 |
| 19843 | rRNA binding | 1 out of 93 genes, 1.1% | RPP0 |
| 8168 | Methyltransferase activity | 1 out of 93 genes, 1.1% | SWD1 |
| 8289 | Lipid binding | 1 out of 93 genes, 1.1% | NUP60 |
| 16829 | Lyase activity | 1 out of 93 genes, 1.1% | CYC3 |
| 16874 | Ligase activity | 1 out of 93 genes, 1.1% | LIP2 |
| 51082 | Unfolded protein binding | 1 out of 93 genes, 1.1% | CNE1 |
| 16791 | Phosphatase activity | 1 out of 93 genes, 1.1% | PHO11 |
| DOWN-REGULATED | |||
| 3674 | Molecular function unknown | 6 out of 16 genes, 37.5% | BSC1, PRM7, YDR246W-A, RRT5, YGL015C, YOR338W |
| 3677 | DNA binding | 3 out of 16 genes, 18.8% | THI2, MGA1, IXR1 |
| 16740 | Transferase activity | 3 out of 16 genes, 18.8% | HOM3, TRA1, URA2 |
| 16874 | Ligase activity | 2 out of 16 genes, 12.5% | SNZ3, URA2 |
| 30234 | Enzyme regulator activity | 1 out of 16 genes, 6.3% | CIP1 |
| 1071 | Nucleic acid binding transcription factor activity | 1 out of 16 genes, 6.3% | MGA1 |
| 16829 | Lyase activity | 1 out of 16 genes, 6.3% | DAL3 |
| 16301 | Kinase activity | 1 out of 16 genes, 6.3% | HOM3 |
| other | Other | 1 out of 16 genes, 6.3% | BTN2 |
| GOID | GO terms (Biological Processes) | Frequency | Gene(s) |
| UP-REGULATED | |||
| 8150 | Biological process unknown | 19 out of 93 genes, 20.4% | AIM2, BDH2, PAU7, YAR023C, UIP3, YAR064W, YAR066W, YAR068W, RRT6, SPG1, YLR255C, YLR264C-A, BOP2, CMG1, YLR278C, YLR281C, YLR283W, YLR287C, YLR326W |
| 51726 | Regulation of cell cycle | 9 out of 93 genes, 9.7% | CCR4, LTE1, CLN3, BUD14, CDC42, RED1, YCS4, MEC3, SFH1 |
| 33043 | Regulation of organelle organization | 8 out of 93 genes, 8.6% | EFB1, LTE1, BUD14, CDC42, EST1, RED1, YCS4, MCM5 |
| 6974 | Cellular response to DNA damage stimulus | 7 out of 93 genes, 7.5% | SAW1, NUP60, IRC20, NEJ1, MCM5, MEC3, SFH1 |
| 7059 | Chromosome segregation | 7 out of 93 genes, 7.5% | LTE1, GIP4, GPN3, RED1, YCS4, NKP2, SFH1 |
| 278 | Mitotic cell cycle | 7 out of 93 genes, 7.5% | CCR4, LTE1, CLN3, CDC42, GPN3, YCS4, SPH1 |
| 42221 | Response to chemical | 6 out of 93 genes, 6.5% | GPB2, CNE1, CDC42, FAR10, SPH1, MID2 |
| 6281 | DNA repair | 6 out of 93 genes, 6.5% | SAW1, NUP60, IRC20, NEJ1, MCM5, SFH1 |
| 6325 | Chromatin organization | 6 out of 93 genes, 6.5% | NUP60, SWD1, YCS4, MCM5, MEC3, SFH1 |
| 2181 | Cytoplasmic translation | 6 out of 93 genes, 6.5% | RBG1, TMA7, RPS28B, RPL38, RPS25B, RPP0 |
| 6605 | Protein targeting | 5 out of 93 genes, 5.4% | VPS8, PEX22, NUP60, GPN3, ERF2 |
| 51052 | Regulation of DNA metabolic process | 5 out of 93 genes, 5.4% | CCR4, SAW1, EST1, MCM5, SFH1 |
| 6366 | Transcription from RNA polymerase II promoter | 5 out of 93 genes, 5.4% | CCR4, GPB2, ECM22, PDR8, SFH1 |
| 48285 | Organelle fission | 5 out of 93 genes, 5.4% | LTE1, CDC42, GPN3, RED1, YCS4 |
| 23052 | Signaling | 5 out of 93 genes, 5.4% | PEX22, GPB2, CDC42, FAR10, MID2 |
| 32200 | Telomere organization | 5 out of 93 genes, 5.4% | SWD1, EST1, MEC3, EST2, YRF1-6 |
| 7010 | Cytoskeleton organization | 4 out of 93 genes, 4.3% | EFB1, ATS1, BUD14, CDC42 |
| 746 | Conjugation | 4 out of 93 genes, 4.3% | CDC42, FAR10, SPH1, MID2 |
| 31399 | Regulation of protein modification process | 4 out of 93 genes, 4.3% | GIP4, CLN3, PEX22, NUP60 |
| 6629 | Lipid metabolic process | 4 out of 93 genes, 4.3% | ECM22, ARV1, ECI1, STT4 |
| 902 | Cell morphogenesis | 4 out of 93 genes, 4.3% | BUD14, CDC42, SPH1, MID2 |
| 6310 | DNA recombination | 4 out of 93 genes, 4.3% | IRC20, MCM5, MEC3, YRF1-6 |
| 51169 | Nuclear transport | 4 out of 93 genes, 4.3% | ECM1, NUP60, GPN3, RPS28B |
| 51321 | Meiotic cell cycle | 4 out of 93 genes, 4.3% | GPB2, RED1, YCS4, GAS2 |
| 6397 | mRNA processing | 3 out of 93 genes, 3.2% | SMD2, YHC1, MID2 |
| 8380 | RNA splicing | 3 out of 93 genes, 3.2% | SMD2, YHC1, MID2 |
| 6401 | RNA catabolic process | 3 out of 93 genes, 3.2% | CCR4, POP5, RPS28B |
| 6260 | DNA replication | 3 out of 93 genes, 3.2% | CCR4, MCM5, SFH1 |
| 7114 | Cell budding | 3 out of 93 genes, 3.2% | ATS1, CDC42, SPH1 |
| 8033 | tRNA processing | 3 out of 93 genes, 3.2% | ATS1, POP5, TAD3 |
| 7124 | Pseudohyphal growth | 3 out of 93 genes, 3.2% | GPB2, CDC42, SPH1 |
| 51049 | Regulation of transport | 3 out of 93 genes, 3.2% | BUD14, ECM22, CDC42 |
| 6364 | rRNA processing | 3 out of 93 genes, 3.2% | MAK16, POP5, DBP9 |
| 70647 | Protein modification by small protein conjugation or removal | 3 out of 93 genes, 3.2% | PEX22, NUP60, UBC12 |
| 42273 | Ribosomal large subunit biogenesis | 3 out of 93 genes, 3.2% | MAK16, DBP9, RPP0 |
| 9451 | RNA modification | 2 out of 93 genes, 2.2% | ATS1, TAD3 |
| 6497 | Protein lipidation | 2 out of 93 genes, 2.2% | ARV1, ERF2 |
| 6869 | Lipid transport | 2 out of 93 genes, 2.2% | ECM22, ARV1 |
| 55085 | Transmembrane transport | 2 out of 93 genes, 2.2% | PEX22, THI7 |
| 70271 | Protein complex biogenesis | 2 out of 93 genes, 2.2% | CYC3, BUD14 |
| 18193 | Peptidyl-amino acid modification | 2 out of 93 genes, 2.2% | NUP60, SWD1 |
| 42594 | Response to starvation | 2 out of 93 genes, 2.2% | RBG1, ECM22 |
| 71554 | Cell wall organization or biogenesis | 2 out of 93 genes, 2.2% | MID2, GAS2 |
| 910 | Cytokinesis | 2 out of 93 genes, 2.2% | BUD14, SPH1 |
| 7033 | Vacuole organization | 2 out of 93 genes, 2.2% | CLN3, CDC42 |
| 6091 | Generation of precursor metabolites and energy | 2 out of 93 genes, 2.2% | RGI2, PIG1 |
| 43934 | Sporulation | 2 out of 93 genes, 2.2% | GPB2, GAS2 |
| 15931 | Nucleobase-containing compound transport | 2 out of 93 genes, 2.2% | NUP60, RPS28B |
| 51186 | Cofactor metabolic process | 2 out of 93 genes, 2.2% | BOL1, COQ11 |
| 6354 | DNA-templated transcription, elongation | 2 out of 93 genes, 2.2% | CCR4, SFH1 |
| 51604 | Protein maturation | 2 out of 93 genes, 2.2% | BOL1, BOL3 |
| 1403 | Invasive growth in response to glucose limitation | 2 out of 93 genes, 2.2% | GPB2, CDC42 |
| 7031 | Peroxisome organization | 2 out of 93 genes, 2.2% | PEX22, PEX30 |
| 6417 | Regulation of translation | 2 out of 93 genes, 2.2% | EFB1, GCD7 |
| 48284 | Organelle fusion | 2 out of 93 genes, 2.2% | CLN3, CDC42 |
| 61025 | Membrane fusion | 2 out of 93 genes, 2.2% | CLN3, CDC42 |
| 5975 | Carbohydrate metabolic process | 1 out of 93 genes, 1.1% | PIG1 |
| 6413 | Translational initiation | 1 out of 93 genes, 1.1% | GCD7 |
| 16570 | Histone modification | 1 out of 93 genes, 1.1% | SWD1 |
| 6468 | Protein phosphorylation | 1 out of 93 genes, 1.1% | CLN3 |
| 16197 | Endosomal transport | 1 out of 93 genes, 1.1% | VPS8 |
| 70925 | Organelle assembly | 1 out of 93 genes, 1.1% | RPP0 |
| 32196 | Transposition | 1 out of 93 genes, 1.1% | YIL082W-A |
| 6887 | Exocytosis | 1 out of 93 genes, 1.1% | CDC42 |
| 6970 | Response to osmotic stress | 1 out of 93 genes, 1.1% | MID2 |
| 43144 | snoRNA processing | 1 out of 93 genes, 1.1% | POP5 |
| 54 | Ribosomal subunit export from nucleus | 1 out of 93 genes, 1.1% | ECM1 |
| 8213 | Protein alkylation | 1 out of 93 genes, 1.1% | SWD1 |
| 6457 | Protein folding | 1 out of 93 genes, 1.1% | CNE1 |
| 6383 | Transcription from RNA polymerase III promoter | 1 out of 93 genes, 1.1% | TFC3 |
| 42255 | Ribosome assembly | 1 out of 93 genes, 1.1% | RPP0 |
| 6414 | Translational elongation | 1 out of 93 genes, 1.1% | EFB1 |
| 7005 | Mitochondrion organization | 1 out of 93 genes, 1.1% | STT4 |
| 32543 | Mitochondrial translation | 1 out of 93 genes, 1.1% | MRPL15 |
| 32787 | Monocarboxylic acid metabolic process | 1 out of 93 genes, 1.1% | ECI1 |
| 16050 | Vesicle organization | 1 out of 93 genes, 1.1% | MST28 |
| 51603 | Proteolysis involved in cellular protein catabolic process | 1 out of 93 genes, 1.1% | CNE1 |
| 6811 | Ion transport | 1 out of 93 genes, 1.1% | CSC1 |
| 6470 | Protein dephosphorylation | 1 out of 93 genes, 1.1% | GIP4 |
| 43543 | Protein acylation | 1 out of 93 genes, 1.1% | ERF2 |
| 55086 | Nucleobase-containing small molecule metabolic process | 1 out of 93 genes, 1.1% | CDD1 |
| 48193 | Golgi vesicle transport | 1 out of 93 genes, 1.1% | ERP1 |
| 6897 | Endocytosis | 1 out of 93 genes, 1.1% | ARV1 |
| 9408 | Response to heat | 1 out of 93 genes, 1.1% | NUP60 |
| other | other | 7 out of 93 genes, 7.5% | YAT1, PHO11, RFU1, LIP2, SYM1, CTS1, ATG39 |
| DOWN-REGULATED | |||
| 6366 | Transcription from RNA polymerase II promoter | 4 out of 16 genes, 25% | THI2, TRA1, IXR1, YOR338W |
| 8150 | Biological process unknown | 4 out of 16 genes, 25% | BSC1, YDR246W-A, RRT5, YGL015C |
| 6520 | Cellular amino acid metabolic process | 2 out of 16 genes, 12.5% | HOM3, URA2 |
| 6974 | Cellular response to DNA damage stimulus | 2 out of 16 genes, 12.5% | TRA1, IXR1 |
| 6766 | Vitamin metabolic process | 2 out of 16 genes, 12.5% | THI2, SNZ3 |
| 6281 | DNA repair | 2 out of 16 genes, 12.5% | TRA1,IXR1 |
| 6468 | Protein phosphorylation | 1 out of 16 genes, 6.3% | CIP1 |
| 16197 | Endosomal transport | 1 out of 16 genes, 6.3% | BTN2 |
| 43543 | Protein acylation | 1 out of 16 genes, 6.3% | TRA1 |
| 6457 | Protein folding | 1 out of 16 genes, 6.3% | BTN2 |
| 55086 | Nucleobase-containing small molecule metabolic process | 1 out of 16 genes, 6.3% | URA2 |
| 51726 | Regulation of cell cycle | 1 out of 16 genes, 6.3% | CIP1 |
| 42221 | Response to chemical | 1 out of 16 genes, 6.3% | IXR1 |
| 43934 | Sporulation | 1 out of 16 genes, 6.3% | YOR338W |
| 18193 | Peptidyl-amino acid modification | 1 out of 16 genes, 6.3% | TRA1 |
| 51321 | Meiotic cell cycle | 1 out of 16 genes, 6.3% | YOR338W |
| 6865 | Amino acid transport | 1 out of 16 genes, 6.3% | BTN2 |
| 746 | Conjugation | 1 out of 16 genes, 6.3% | PRM7 |
| 31399 | Regulation of protein modification process | 1 out of 16 genes, 6.3% | CIP1 |
| 278 | Mitotic cell cycle | 1 out of 16 genes, 6.3% | CIP1 |
| 16570 | Histone modification | 1 out of 16 genes, 6.3% | TRA1 |
| 6325 | Chromatin organization | 1 out of 16 genes, 6.3% | TRA1 |
| 6811 | Ion transport | 1 out of 16 genes, 6.3% | BTN2 |
| other | Other | 2 out of 16 genes, 12.5% | MGA1, DAL3 |